Estimation of electronic coupling in π -stacked donor-bridge-acceptor systems: correction of the two-state model

Comparison of donor-acceptor electronic couplings calculated within two-state and three-state models suggests that the two-state treatment can provide unreliable estimates of Vda because of neglecting the multistate effects. We show that in most cases accurate values of the electronic coupling in a π stack, where donor and acceptor are separated by a bridging unit, can be obtained as Ṽ da = (E2 - E1) μ12 Rda + (2 E3 - E1 - E2) 2 μ13 μ23 Rda2, where E1, E2, and E3 are adiabatic energies of the ground, charge-transfer, and bridge states, respectively, μij is the transition dipole moments between the states i and j, and Rda is the distance between the planes of donor and acceptor. In this expression based on the generalized Mulliken-Hush approach, the first term corresponds to the coupling derived within a two-state model, whereas the second term is the superexchange correction accounting for the bridge effect. The formula is extended to bridges consisting of several subunits. The influence of the donor-acceptor energy mismatch on the excess charge distribution, adiabatic dipole and transition moments, and electronic couplings is examined. A diagnostic is developed to determine whether the two-state approach can be applied. Based on numerical results, we showed that the superexchange correction considerably improves estimates of the donor-acceptor coupling derived within a two-state approach. In most cases when the two-state scheme fails, the formula gives reliable results which are in good agreement (within 5%) with the data of the three-state generalized Mulliken-Hush model

Which economic model for a water-efficient Europe? Report of a CEPS Task Force. CEPS Task Force Report, 27 November 2012

This CEPS Task Force Report focuses on how to improve water efficiency in Europe, notably in public supply, households, agriculture, energy and manufacturing as well as across sectors. It presents a number of recommendations on how to make better use of economic policy instruments to sustainably manage the EU’s water resources. Published in the run-up to the European Commission’s “Blueprint to Safeguard Europe’s Waters”, the report contributes to the policy deliberations in two ways. First, by assessing the viability of economic policy instruments, it addresses a major shortcoming that has so far prevented the 2000 EU Water Framework Directive (WFD) from becoming fully effective in practice: the lack of appropriate, coherent and effective instruments in (some) member states. Second, as the Task Force report is the result of an interactive process involving a variety of stakeholders, it is able to point to the key differences in interpreting and applying WFD principles that have led to a lack of policy coherence across the EU and to offer some pragmatic advice on moving forward.

Monitoring present day changes in water vapour and the radiative energy balance using satellite data, reanalyses and models

A combination of satellite data, reanalysis products and climate models are combined to monitor changes in water vapour, clear-sky radiative cooling of the atmosphere and precipitation over the period 1979-2006. Climate models are able to simulate observed increases in column integrated water vapour (CWV) with surface temperature (Ts) over the ocean. Changes in the observing system lead to spurious variability in water vapour and clear-sky longwave radiation in reanalysis products. Nevertheless all products considered exhibit a robust increase in clear-sky longwave radiative cooling from the atmosphere to the surface; clear-sky longwave radiative cooling of the atmosphere is found to increase with Ts at the rate of ~4 Wm-2 K-1 over tropical ocean regions of mean descending vertical motion. Precipitation (P) is tightly coupled to atmospheric radiative cooling rates and this implies an increase in P with warming at a slower rate than the observed increases in CWV. Since convective precipitation depends on moisture convergence, the above implies enhanced precipitation over convective regions and reduced precipitation over convectively suppressed regimes. To quantify this response, observed and simulated changes in precipitation rate are analysed separately over regions of mean ascending and descending vertical motion over the tropics. The observed response is found to be substantially larger than the model simulations and climate change projections. It is currently not clear whether this is due to deficiencies in model parametrizations or errors in satellite retrievals.

Evaluation of the Met Office global forecast model using Geostationary Earth Radiation Budget (GERB) data

Simulations of the top-of-atmosphere radiative-energy budget from the Met Office global numerical weather-prediction model are evaluated using new data from the Geostationary Earth Radiation Budget (GERB) instrument on board the Meteosat-8 satellite. Systematic discrepancies between the model simulations and GERB measurements greater than 20 Wm-2 in outgoing long-wave radiation (OLR) and greater than 60 Wm-2 in reflected short-wave radiation (RSR) are identified over the period April-September 2006 using 12 UTC data. Convective cloud over equatorial Africa is spatially less organized and less reflective than in the GERB data. This bias depends strongly on convective-cloud cover, which is highly sensitive to changes in the model convective parametrization. Underestimates in model OLR over the Gulf of Guinea coincide with unrealistic southerly cloud outflow from convective centres to the north. Large overestimates in model RSR over the subtropical ocean, greater than 50 Wm-2 at 12 UTC, are explained by unrealistic radiative properties of low-level cloud relating to overestimation of cloud liquid water compared with independent satellite measurements. The results of this analysis contribute to the development and improvement of parametrizations in the global forecast model.

How many facets are needed to represent the surface energy balance of an urban area?

We investigate the question of how many facets are needed to represent the energy balance of an urban area by developing simplified 3-, 2- and 1-facet versions of a 4-facet energy balance model of two-dimensional streets and buildings. The 3-facet model simplifies the 4-facet model by averaging over the canyon orientation, which results in similar net shortwave and longwave balances for both wall facets, but maintains the asymmetry in the heat fluxes within the street canyon. For the 2-facet model, on the assumption that the wall and road temperatures are equal, the road and wall facets can be combined mathematically into a single street-canyon facet with effective values of the heat transfer coefficient, albedo, emissivity and thermodynamic properties, without further approximation. The 1-facet model requires the additional assumption that the roof temperature is also equal to the road and wall temperatures. Idealised simulations show that the geometry and material properties of the walls and road lead to a large heat capacity of the combined street canyon, whereas the roof behaves like a flat surface with low heat capacity. This means that the magnitude of the diurnal temperature variation of the street-canyon facets are broadly similar and much smaller than the diurnal temperature variation of the roof facets. Consequently, the approximation that the street-canyon facets have similar temperatures is sound, and the road and walls can be combined into a single facet. The roof behaves very differently and a separate roof facet is required. Consequently, the 2-facet model performs similarly to the 4-facet model, while the 1-facet model does not. The models are compared with previously published observations collected in Mexico City. Although the 3- and 2-facet models perform better than the 1-facet model, the present models are unable to represent the phase of the sensible heat flux. This result is consistent with previous model comparisons, and we argue that this feature of the data cannot be produced by a single column model. We conclude that a 2-facet model is necessary, and for numerical weather prediction sufficient, to model an urban surface, and that this conclusion is robust and therefore applicable to more general geometries.

Climate entropy budget of the HadCM3 atmosphere-ocean general circulation model and of FAMOUS, its low resolution version

The entropy budget is calculated of the coupled atmosphere–ocean general circulation model HadCM3. Estimates of the different entropy sources and sinks of the climate system are obtained directly from the diabatic heating terms, and an approximate estimate of the planetary entropy production is also provided. The rate of material entropy production of the climate system is found to be ∼50 mW m−2 K−1, a value intermediate in the range 30–70 mW m−2 K−1 previously reported from different models. The largest part of this is due to sensible and latent heat transport (∼38 mW m−2 K−1). Another 13 mW m−2 K−1 is due to dissipation of kinetic energy in the atmosphere by friction and Reynolds stresses. Numerical entropy production in the atmosphere dynamical core is found to be about 0.7 mW m−2 K−1. The material entropy production within the ocean due to turbulent mixing is ∼1 mW m−2 K−1, a very small contribution to the material entropy production of the climate system. The rate of change of entropy of the model climate system is about 1 mW m−2 K−1 or less, which is comparable with the typical size of the fluctuations of the entropy sources due to interannual variability, and a more accurate closure of the budget than achieved by previous analyses. Results are similar for FAMOUS, which has a lower spatial resolution but similar formulation to HadCM3, while more substantial differences are found with respect to other models, suggesting that the formulation of the model has an important influence on the climate entropy budget. Since this is the first diagnosis of the entropy budget in a climate model of the type and complexity used for projection of twenty-first century climate change, it would be valuable if similar analyses were carried out for other such models.

Monitoring changes in precipitation and radiative energy using satellite data and climate models

Current changes in the tropical hydrological cycle, including water vapour and precipitation, are presented over the period 1979-2008 based on a diverse suite of observational datasets and atmosphere-only climate models. Models capture the observed variability in tropical moisture while reanalyses cannot. Observed variability in precipitation is highly dependent upon the satellite instruments employed and only cursory agreement with model simulations, primarily relating to the interannual variability associated with the El Niño Southern Oscillation. All datasets display a positive relationship between precipitation and surface temperature but with a large spread. The tendency for wet, ascending regions to become wetter at the expense of dry, descending regimes is in general reproduced. Finally, the frequency of extreme precipitation is shown to rise with warming in the observations and for the model ensemble mean but with large spread in the model simulations. The influence of the Earth’s radiative energy balance in relation to changes in the tropical water cycle are discussed

A surface energy perspective on climate change

A surface forcing response framework is developed that enables an understanding of time-dependent climate change from a surface energy perspective. The framework allows the separation of fast responses that are unassociated with global-mean surface air temperature change (ΔT), which is included in the forcing, and slow feedbacks that scale with ΔT. The framework is illustrated primarily using 2 × CO2 climate model experiments and is robust across the models. For CO2 increases, the positive downward radiative component of forcing is smaller at the surface than at the tropopause, and so a rapid reduction in the upward surface latent heat (LH) flux is induced to conserve the tropospheric heat budget; this reduces the precipitation rate. Analysis of the time-dependent surface energy balance over sea and land separately reveals that land areas rapidly regain energy balance, and significant land surface warming occurs before global sea temperatures respond. The 2 × CO2 results are compared to a solar increase experiment and show that some fast responses are forcing dependent. In particular, a significant forcing from the fast hydrological response found in the CO2 experiments is much smaller in the solar experiment. The different fast response explains why previous equilibrium studies found differences in the hydrological sensitivity between these two forcings. On longer time scales, as ΔT increases, the net surface longwave and LH fluxes provide positive and negative surface feedbacks, respectively, while the net surface shortwave and sensible heat fluxes change little. It is found that in contrast to their fast responses, the longer-term response of both surface energy fluxes and the global hydrological cycle are similar for the different forcing agents.

The physical properties of the atmosphere in the new Hadley Centre Global Environmental Model (HadGEM1). Part II: Aspects of variability and regional climate

The performance of the atmospheric component of the new Hadley Centre Global Environmental Model (HadGEM1) is assessed in terms of its ability to represent a selection of key aspects of variability in the Tropics and extratropics. These include midlatitude storm tracks and blocking activity, synoptic variability over Europe, and the North Atlantic Oscillation together with tropical convection, the Madden-Julian oscillation, and the Asian summer monsoon. Comparisons with the previous model, the Third Hadley Centre Coupled Ocean-Atmosphere GCM (HadCM3), demonstrate that there has been a considerable increase in the transient eddy kinetic energy (EKE), bringing HadGEM1 into closer agreement with current reanalyses. This increase in EKE results from the increased horizontal resolution and, in combination with the improved physical parameterizations, leads to improvements in the representation of Northern Hemisphere storm tracks and blocking. The simulation of synoptic weather regimes over Europe is also greatly improved compared to HadCM3, again due to both increased resolution and other model developments. The variability of convection in the equatorial region is generally stronger and closer to observations than in HadCM3. There is, however, still limited convective variance coincident with several of the observed equatorial wave modes. Simulation of the Madden-Julian oscillation is improved in HadGEM1: both the activity and interannual variability are increased and the eastward propagation, although slower than observed, is much better simulated. While some aspects of the climatology of the Asian summer monsoon are improved in HadGEM1, the upper-level winds are too weak and the simulation of precipitation deteriorates. The dominant modes of monsoon interannual variability are similar in the two models, although in HadCM3 this is linked to SST forcing, while in HadGEM1 internal variability dominates. Overall, analysis of the phenomena considered here indicates that HadGEM1 performs well and, in many important respects, improves upon HadCM3. Together with the improved representation of the mean climate, this improvement in the simulation of atmospheric variability suggests that HadGEM1 provides a sound basis for future studies of climate and climate change.

El Nino-mean state-seasonal cycle interactions in a multi-model ensemble

The modelled El Nino-mean state-seasonal cycle interactions in 23 coupled ocean-atmosphere GCMs, including the recent IPCC AR4 models, are assessed and compared to observations and theory. The models show a clear improvement over previous generations in simulating the tropical Pacific climatology. Systematic biases still include too strong mean and seasonal cycle of trade winds. El Nino amplitude is shown to be an inverse function of the mean trade winds in agreement with the observed shift of 1976 and with theoretical studies. El Nino amplitude is further shown to be an inverse function of the relative strength of the seasonal cycle. When most of the energy is within the seasonal cycle, little is left for inter-annual signals and vice versa. An interannual coupling strength (ICS) is defined and its relation with the modelled El Nino frequency is compared to that predicted by theoretical models. An assessment of the modelled El Nino in term of SST mode (S-mode) or thermocline mode (T-mode) shows that most models are locked into a S-mode and that only a few models exhibit a hybrid mode, like in observations. It is concluded that several basic El Nino-mean state-seasonal cycle relationships proposed by either theory or analysis of observations seem to be reproduced by CGCMs. This is especially true for the amplitude of El Nino and is less clear for its frequency. Most of these relationships, first established for the pre-industrial control simulations, hold for the double and quadruple CO2 stabilized scenarios. The models that exhibit the largest El Nino amplitude change in these greenhouse gas (GHG) increase scenarios are those that exhibit a mode change towards a T-mode (either from S-mode to hybrid or hybrid to T-mode). This follows the observed 1976 climate shift in the tropical Pacific, and supports the-still debated-finding of studies that associated this shift to increased GHGs. In many respects, these models are also among those that best simulate the tropical Pacific climatology (ECHAM5/MPI-OM, GFDL-CM2.0, GFDL-CM2.1, MRI-CGM2.3.2, UKMO-HadCM3). Results from this large subset of models suggest the likelihood of increased El Nino amplitude in a warmer climate, though there is considerable spread of El Nino behaviour among the models and the changes in the subsurface thermocline properties that may be important for El Nino change could not be assessed. There are no clear indications of an El Nino frequency change with increased GHG.

Performance of the OPA/ARPEGE-T21 global ocean-atmosphere coupled model

The climatology of the OPA/ARPEGE-T21 coupled general circulation model (GCM) is presented. The atmosphere GCM has a T21 spectral truncation and the ocean GCM has a 2°×1.5° average resolution. A 50-year climatic simulation is performed using the OASIS coupler, without flux correction techniques. The mean state and seasonal cycle for the last 10 years of the experiment are described and compared to the corresponding uncoupled experiments and to climatology when available. The model reasonably simulates most of the basic features of the observed climate. Energy budgets and transports in the coupled system, of importance for climate studies, are assessed and prove to be within available estimates. After an adjustment phase of a few years, the model stabilizes around a mean state where the tropics are warm and resemble a permanent ENSO, the Southern Ocean warms and almost no sea-ice is left in the Southern Hemisphere. The atmospheric circulation becomes more zonal and symmetric with respect to the equator. Once those systematic errors are established, the model shows little secular drift, the small remaining trends being mainly associated to horizontal physics in the ocean GCM. The stability of the model is shown to be related to qualities already present in the uncoupled GCMs used, namely a balanced radiation budget at the top-of-the-atmosphere and a tight ocean thermocline.

A potential energy surface for the ground state of formaldehyde, H2CO(1A1)

A model potential energy function for the ground state of H2CO has been derived which covers the whole space of the six internal coordinates. This potential reproduces the experimental energy, geometry and quadratic force field of formaldehyde, and dissociates correctly to all possible atom, diatom and triatom fragments. Thus there are good reasons for believing it to be close to the true potential energy surface except in regions where both hydrogen atoms are close to the oxygen. It leads to the prediction that there should be a metastable singlet hydroxycarbene HCOH which has a planar trans structure and an energy of 2•31 eV above that of equilibrium formaldehyde. The reaction path for dissociation into H2 + CO is predicted to pass through a low symmetry transition state with an activation energy of 4•8 eV. Both of these predictions are in good agreement with recently published ab initio calculations.

Potential energy surface intersections in triatomic molecules

The different types of surface intersection which may occur in linear configurations of triatomic molecules are reviewed, particularly with regard to the way in which the degeneracy is split as the molecule bends. The Renner-Teller effect in states of symmetry Π, Δ, Φ, etc., and intersections between Σ and Π, Σ and Δ, and Π and Δ states are discussed. A general method of modelling such intersecting potential surfaces is proposed, as a development of the model previously used by Murrell and Carter and co-workers for single-valued surfaces. Some of the lower energy surfaces of H2O, NH2, O3, C3, and HNO are discussed as examples.

Results of a mechanistic model estimating methane in relation to methane emissions measured in dairy cows

This investigation determines the accuracy of estimation of methanogenesis by a dynamic mechanistic model with real data determined in a respiration trial, where cows were fed a wide range of different carbohydrates included in the concentrates. The model was able to predict ECM (Energy corrected milk) very well, while the NDF digestibility of fibrous feed was less well predicted. Methane emissions were predicted quite well, with the exception of one diet containing wheat. The mechanistic model is therefore a helpful tool to estimate methanogenesis based on chemical analysis and dry matter intake, but the prediction can still be improved.

Benchmarking consensus model quality assessment for protein fold recognition

Background: Selecting the highest quality 3D model of a protein structure from a number of alternatives remains an important challenge in the field of structural bioinformatics. Many Model Quality Assessment Programs (MQAPs) have been developed which adopt various strategies in order to tackle this problem, ranging from the so called "true" MQAPs capable of producing a single energy score based on a single model, to methods which rely on structural comparisons of multiple models or additional information from meta-servers. However, it is clear that no current method can separate the highest accuracy models from the lowest consistently. In this paper, a number of the top performing MQAP methods are benchmarked in the context of the potential value that they add to protein fold recognition. Two novel methods are also described: ModSSEA, which based on the alignment of predicted secondary structure elements and ModFOLD which combines several true MQAP methods using an artificial neural network. Results: The ModSSEA method is found to be an effective model quality assessment program for ranking multiple models from many servers, however further accuracy can be gained by using the consensus approach of ModFOLD. The ModFOLD method is shown to significantly outperform the true MQAPs tested and is competitive with methods which make use of clustering or additional information from multiple servers. Several of the true MQAPs are also shown to add value to most individual fold recognition servers by improving model selection, when applied as a post filter in order to re-rank models. Conclusion: MQAPs should be benchmarked appropriately for the practical context in which they are intended to be used. Clustering based methods are the top performing MQAPs where many models are available from many servers; however, they often do not add value to individual fold recognition servers when limited models are available. Conversely, the true MQAP methods tested can often be used as effective post filters for re-ranking few models from individual fold recognition servers and further improvements can be achieved using a consensus of these methods.